An international team of scientists has sequenced and assembled the genome of the Basenji dog (Canis lupus familiaris), an ancient dog breed of central African origins that still lives and hunts with tribesmen in Congo. The genome of the Basenji, which sits at the base of the dog breed family tree, makes an excellent unbiased reference for future comparisons between dog breeds and evolutionary analysis of dogs.

The Basenji dog (Canis lupus familiaris).

Dogs were the first animals to be domesticated by humans some 30,000 years ago and exhibit exceptional levels of breed variation as a result of extensive artificial trait selection.

It is not clear whether they were domesticated once or several times, though the weight of accumulating evidence suggests multiple events.

By establishing genome resources for more ancient dog breeds, scientists can explore genetic adaptations perhaps unique to the modern dog breeds.

The Basenji dog is an ancient breed that sits at the base of the currently accepted dog family tree.

Basenji-like dogs are depicted in drawings and models dating back to the 12th dynasty of Egypt and they share many unique traits with pariah dog types.

Like dingoes and New Guinea singing dogs, Basenjis come into oestrus annually — as compared to most other dog breeds, which have two or more breeding seasons every year. These three breeds are prone to howls, yodels, and other vocalizations over the characteristic bark of modern breeds.

Nicknamed the barkless dog, Basenjis were originally indigenous to central Africa, wherever there was tropical forest. Primarily, what is now the DRC Congo, Southern Sudan, Central African Republic and the small countries on the central Atlantic coast.

Today their territory has shrunk to the more remote parts of central Africa.

The Basenjis probably made their debut in the Western world in around 1843. In a painting of three dogs belonging to Queen Victoria and Prince Albert entitled ‘Esquimaux, Niger and Neptune,’ Niger is clearly a Basenji.

“The dog was probably the first animal to be domesticated by humans and has subsequently been artificially selected by humans into a great diversity of dog breeds of different sizes and shapes,” said Dr. Richard Edwards, a researcher in the School of Biotechnology and Biomolecular Sciences at the University of New South Wales.

“Before this paper, it was difficult to interpret differences between the dog reference genomes and non-domesticated dogs, such as dingoes, jackals, coyotes, wolves and foxes.”

“Big changes could be the result of recent artificial selection during creation of the specific reference breed.”

“By adding such a high-quality genome at the base of the domestic dog family tree, we have provided an anchor point for studies that can help establish the timing and direction of genetic changes during domestication and subsequent breeding.”

“As Basenjis are a very old breed, they provide the perfect comparison to more modern breeds to explore how breeds were developed, the process of domestication and assist in studies looking for disease genes,” said Dr. Kylie Cairns, a researcher in the School of Biological, Earth and Environmental Sciences at the University of New South Wales.

“This genome will also be critical in comparisons to wolves, dingoes and village dogs as an example of an ancient domestic breed.”

The researchers sequenced the genomes of two Basenjis: a female, China, and a male, Wags.

“Over 99% of the final genome assembly can be found in the 39 pieces that represent the 39 dog chromosomes,” Dr. Edwards said.

“These chromosomes only have one hundred regions of unresolved sequence, which is the fewest of any published dog genome so far.”

“This makes it one of the highest-quality dog genomes produced to date.”

The scientists also conducted pairwise comparisons and analyzed structural variations between assembled genomes of three dog breeds: Basenji, Boxer and German shepherd dog.

“The Basenji genome sequence is different to the traditional dog reference genome, CanFam, which is of a highly-derived breed, the Boxer,” Dr. Edwards said.

“The choice of dog reference genome can affect the results of future dog genetics studies looking at genetic variants.”

“The Basenji genome may allow scientists to more fully unravel the evolutionary history of early dogs and how humans have shaped the first dogs into the companions and breeds we have today,” Dr. Cairns added.

“Many people wouldn’t realize that most dog breeds arose in the last 200-300 years.”

“So having access to a high quality reference genome from an ancient breed such as the Basenji gives insight into early breed development and how domestic dogs have been shaped by humans in the last few thousand years.”

“We will also be able to tackle lingering questions about the evolutionary history of dingoes and their relatives in New Guinea, with the Basenji acting as a halfway point between non-domesticated dingoes and truly modern dog breeds like pugs, kelpies and poodles.”

The results were published March 2021 in the journal BMC Genomics.

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R.J. Edwards et al. 2021. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 22, 188; doi: 10.1186/s12864-021-07493-6